Interesting. Our contribution to monitoring DNS is to make sure our HTTP uptime checker runs over both ipv4 AND ipv6 as separate checks. That way if we mess up our AAAA record but not our A record (or vice versa) we still get a fail. I've looked at some commercial SAAS uptime checkers and no-one seems to offer this as a feature - have I missed one that does?
The way to do this in Prometheus is to use the following settings on the blackbox module:
[ preferred_ip_protocol: <string> | default = "ip6" ]
[ ip_protocol_fallback: <boolean> | default = true ]
So you need 2 modules, one for each ip version. As for automating setting these up, we deploy our Prometheus server with salt so we can use Jinja templating in all our Prometheus config files. That really cuts down on repeating boiler plate code.
This is also interesting for other reasons; in host downtime situations you can sometime see they will drop one type of traffic and not the other.